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Estimated (re-scaled) false positive rate (upper) and the false negative rates (lower), using the mutations across whole exome (‘exome’) or within the 76 genes (‘76genes’) in the LUSC benchmark data. We applied four approaches: validation using the gold-standard deep-sequencing data (‘byGS’), the RNA-seq validation method (‘byRNA-seq’), the pseudo-validation method (‘byPseudo’), and the latent class models (‘byLatent’).
